[med-svn] [Git][med-team/tiddit][upstream] New upstream version 3.5.1+dfsg

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch upstream at Debian Med / tiddit


Commits:
228e8323 by Nilesh Patra at 2023-01-29T14:59:29+05:30
New upstream version 3.5.1+dfsg
- - - - -


4 changed files:

- README.md
- setup.py
- tiddit/__main__.py
- tiddit/tiddit_coverage_analysis.pyx


Changes:

=====================================
README.md
=====================================
@@ -42,23 +42,13 @@ TIDDIT may be installed using bioconda:
 ```
 conda install tiddit
 ```
-	
-Next, you may run TIDDIT like this:
-```
-tiddit --help
-tiddit --sv
-tiddit --cov
-```
 
-TIDDIT is also distributed with a Docker container (http://singularity.lbl.gov/index.html). Type the following command to download the container:
+or using the docker image on biocontainers
 ```
-singularity pull --name TIDDIT.simg 
+docker pull quay.io/biocontainers/tiddit:<tag>
 ```
+visit https://quay.io/repository/biocontainers/tiddit?tab=tags for tags.
 
-Type the following to run tiddit:
-```
-singularity exec TIDDIT.simg tiddit
-```
 
 The SV module
 =============


=====================================
setup.py
=====================================
@@ -20,7 +20,7 @@ else:
 
 setup(
     name = 'tiddit',
-    version = '3.4.0',
+    version = '3.5.1',
 
     url = "https://github.com/SciLifeLab/TIDDIT",
     author = "Jesper Eisfeldt",


=====================================
tiddit/__main__.py
=====================================
@@ -17,7 +17,7 @@ import tiddit.tiddit_variant as tiddit_variant
 import tiddit.tiddit_contig_analysis as tiddit_contig_analysis
 
 def main():
-	version="3.4.0"
+	version="3.5.1"
 	parser = argparse.ArgumentParser("""tiddit-{}""".format(version),add_help=False)
 	parser.add_argument("--sv"	 , help="call structural variation", required=False, action="store_true")
 	parser.add_argument("--cov"        , help="generate a coverage bed file", required=False, action="store_true")
@@ -115,11 +115,8 @@ def main():
 			i+=1
 
 		prefix=args.o
-		try:
-			os.mkdir( "{}_tiddit".format(prefix) )
-			os.mkdir("{}_tiddit/clips".format(prefix) )
-		except:
-			print("Folder already exists")
+		os.mkdir(f"{prefix}_tiddit")
+		os.mkdir(f"{prefix}_tiddit/clips")
 
 		pysam.index("-c","-m","6","-@",str(args.threads),bam_file_name,"{}_tiddit/{}.csi".format(args.o,sample_id))
 


=====================================
tiddit/tiddit_coverage_analysis.pyx
=====================================
@@ -1,4 +1,5 @@
 import numpy
+import re
 cimport numpy
 import pysam
 import gzip
@@ -19,7 +20,9 @@ def get_gc(str reference_fasta,bam_header,bin_size):
 		with gzip.open(reference_fasta, 'r') as f:
 			sequence=f.read()
 
-	split_reference=sequence.split(">")
+
+	#split_reference=sequence.split(">")
+	split_reference=re.split("\n>|^>", sequence)
 	del sequence
 	del split_reference[0]
 



View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/commit/228e83238ce14f577ef3a6e6bd35afa86d4d533e

-- 
View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/commit/228e83238ce14f577ef3a6e6bd35afa86d4d533e
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